GilsonLabUCSD / pAPRika

Advanced toolkit for binding free energy calculations

BSD 3-Clause "New" or "Revised" License

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Refactor build related modules #157

Closed jeff231li closed 3 years ago

jeff231li commented 3 years ago

Grouped align.py, dummy.py, and tleap.py into the same namespace paprika.build.
Changed class name of tleap.py from System to TLeap.
Added a function to specify water models and the correct library, frcmod, and waterbox will be written to the tleap input file.
Moved test_add_dummy function from test_tleap.py to test_dummy.py (seems more appropriate).
Update the tutorials and README to reflect the changes in the namespace

lgtm-com[bot] commented 3 years ago

This pull request introduces 1 alert and fixes 1 when merging 86a51b5aa9f4c02e163492f9963356f14d52da35 into fcab626283148afa58fc24f0ed35a828e0e133bf - view on LGTM.com

new alerts:

1 for Except block handles 'BaseException'

fixed alerts:

1 for Except block handles 'BaseException'

codecov-io commented 3 years ago

Codecov Report

Merging #157 (2062a02) into master (fcab626) will increase coverage by 0.10%. The diff coverage is 87.04%.

lgtm-com[bot] commented 3 years ago

This pull request introduces 1 alert and fixes 1 when merging 2062a02dadaf980e17ead5a1bff59fd5acb24a94 into fcab626283148afa58fc24f0ed35a828e0e133bf - view on LGTM.com

new alerts:

1 for Except block handles 'BaseException'

fixed alerts:

1 for Except block handles 'BaseException'